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Structure of LIMK1 Kinase domain with allosteric inhibitor TH-470
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.2M Ammonium Citrate dibasic, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.692 α = 90 b = 83.665 β = 91.97 c = 96.513 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2019-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 51.2 99.9 0.221 0.239 0.091 0.987 7 6.8 33406
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.94 99.9 1.452 1.57 0.595 0.59 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5NXC 2.8 50.15 31818 1574 99.91 0.2094 0.2057 0.21 0.2862 0.2829 RANDOM 45.413
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -1.56 -0.15 -2.97 4.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.039 r_dihedral_angle_4_deg 18.296 r_dihedral_angle_3_deg 17.125 r_dihedral_angle_1_deg 6.681 r_angle_refined_deg 1.425 r_angle_other_deg 1.165 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.039 r_dihedral_angle_4_deg 18.296 r_dihedral_angle_3_deg 17.125 r_dihedral_angle_1_deg 6.681 r_angle_refined_deg 1.425 r_angle_other_deg 1.165 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8464 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction xia2 data reduction